Whole genome sequence and a phylogenetic analysis of the G8P[14] group A rotavirus strain from roe deer

Epidemiological study of unusual rotavirus strains and molecular characterization of emerging P[14] strains isolated from children with acute gastroenteritis during a 15-year period

Rotavirus group A (RVA) is characterized by molecular and epidemiological diversity. To date, 42 G and 58 P RVA genotypes have been identified, some of which, like P[14], have a zoonotic origin. In this study, we describe the epidemiology of unusual RVA genotypes and the molecular characteristics of P[14] strains. Fecal samples from children ≤ 16 years of age with acute gastroenteritis (AGE) who were hospitalized during 2007-2021 in Greece were tested for RVA by immunochromatography. Positive RVA samples were G and P genotyped, and part of the VP7 and VP4 genes were sequenced by the Sanger method. Epidemiological data were also recorded. Phylogenetic analysis of P[14] was performed using MEGA 11 software. Sixty-two (1.4%) out of 4427 children with RVA AGE were infected with an unusual G (G6/G8/G10) or P (P[6]/P[9]/P[10]/P[11]/P[14]) genotype. Their median (IQR) age was 18.7 (37.3) months, and 67.7% (42/62) were males. None of the children were vaccinated against RVA. P[9] (28/62; 45.2%) was the most common unusual genotype, followed by P[14] (12/62; 19.4%). In the last two years, during the period of the COVID-19 pandemic, an emergence of P[14] was observed (5/12, 41.6%) after an 8-year absence. The highest prevalence of P[14] infection was seen in the spring (91.7%). The combinations G8P[14] (41.7%), G6P[14] (41.7%), and G4P[14] (16.6%) were also detected. Phylogenetic analysis showed a potential evolutionary relationship of three human RVA P[14] strains to a fox strain from Croatia. These findings suggest a possible zoonotic origin of P[14] and interspecies transmission between nondomestic animals and humans, which may lead to new RVA genotypes with unknown severity.

Rotaviruses in Wild Ungulates from Germany, 2019-2022

Rotavirus A (RVA) is an important cause of diarrhea in humans and animals. However, RVA in wild animals has only scarcely been investigated so far. Here, the presence of RVA in wild ungulates hunted between 2019 and 2022 in Brandenburg, Germany, was investigated using real-time RT-PCR and sequencing of RT-PCR products. By analyzing intestinal contents, RVA-RNA was detected in 1.0% (2/197) of wild boar (Sus scrofa), 1.3% (2/152) of roe deer (Capreolus capreolus), and 2.1% (2/95) of fallow deer (Dama dama) but not in 28 red deer (Cervus elaphus) samples. Genotyping identified G3P[13] strains in wild boar, which were closely related to previously described pig and wild boar strains. Genotype G10P[15] strains, closely related to strains from roe deer, sheep, or cattle, were found in roe deer. The strains of fallow deer represented genotype G3P[3], clustering in a group containing different strains from several hosts. The results indicated a low prevalence of RVA in wild ungulates in Germany. Associations of specific genotypes with certain ungulate species seem to exist but should be confirmed by analyses of more samples in the future.

Codon usage of host-specific P genotypes (VP4) in group A rotavirus

Background

Group A rotavirus (RVA) is a common causative agent of acute gastroenteritis in infants and young children worldwide. RVA P genotypes, determined by VP4 sequences, have been confirmed to infect humans and animals. However, their codon usage patterns that are essential to obtain insights into the viral evolution, host adaptability, and genetic characterization remained unclear, especially across animal hosts.

Results

We performed a comprehensive codon usage analysis of eight host-specific RVA P genotypes, including human RVA (P[4] and P[8]), porcine RVA (P[13] and P[23]), and zoonotic RVA (P[1], P[6], P[7] and P[19]), based on 233 VP4 complete coding sequences. Nucleotide composition, relative synonymous codon usage (RSCU), and effective number of codons (ENC) were calculated. Principal component analysis (PCA) based on RSCU values was used to explore the codon usage patterns of different RVA P genotypes. In addition, mutation pressure and natural selection were identified by using ENC-plot, parity rule 2 plot, and neutrality plot analyses. All VP4 sequences preferred using A/U nucleotides (A: 0.354-0.377, U: 0.267-0.314) than G/C nucleotides across genotypes. Similarly, majority of commonly used synonymous codons were likely to end with A/U nucleotides (A: 9/18-12/18, U: 6/18-9/18). In PCA, human, porcine, and zoonotic genotypes clustered separately in terms of RSCU values, indicating the host-specific codon usage patterns; however, porcine and zoonotic genotypes were partly overlapped. Human genotypes, P[4] and P[8], had stronger codon usage bias, as indicated by more over-represented codons and lower ENC, compared to porcine and zoonotic genotypes. Moreover, natural selection was determined to be a predominant driver in shaping the codon usage bias across the eight P genotypes. In addition, mutation pressure contributed to the codon usage bias of human genotypes.

Conclusions

Our study identified a strong codon usage bias of human RVA P genotypes attributable to both natural selection and mutation pressure, whereas similar codon usage bias between porcine and zoonotic genotypes predominantly attributable to natural selection. It further suggests possible cross-species transmission. Therefore, it warrants further surveillance of RVA P genotypes for early identification of zoonotic infection.

Supplementary Information

The online version contains supplementary material available at 10.1186/s12864-022-08730-2.

Effect of rotavirus genetic diversity on vaccine impact

Group A rotaviruses (RVAs) are the leading cause of gastroenteritis, causing 0.2 million deaths and several million hospitalisations globally each year. Four rotavirus vaccines (Rotarix^TM , RotaTeq^TM , Rotavac^® and ROTASIIL^® ) have been pre-qualified by the World Health Organization (WHO), but the two newly pre-qualified vaccines (Rotavac^® and ROTASIIL^® ) are currently only in use in Palestine and India, respectively. In 2009, WHO strongly proposed that rotavirus vaccines be included in the routine vaccination schedule of all countries around the world. By the end of 2019, a total of 108 countries had administered rotavirus vaccines, and 10 countries have currently been approved by Gavi for the introduction of rotavirus vaccine in the near future. With 39% of global coverage, rotavirus vaccines have had a substantial effect on diarrhoeal morbidity and mortality in different geographical areas, although efficacy appears to be higher in high income settings. Due to the segmented RNA genome, the pattern of RVA genotypes in the human population is evolving through interspecies transmission and/or reassortment events for which the vaccine might be less effective in the future. However, despite the relative increase in some particular genotypes after rotavirus vaccine use, the overall efficacy of rotavirus mass vaccination worldwide has not been affected. Some of the challenges to improve the effect of current rotavirus vaccines can be solved in the future by new rotavirus vaccines and by vaccines currently in progress.

Epidemiology and Molecular Characterization of Rotavirus A in Fruit Bats in Bangladesh

Rotavirus A (RVA) is the primary cause of acute dehydrating diarrhea in human and numerous animal species. Animal-to-human interspecies transmission is one of the evolutionary mechanisms driving rotavirus strain diversity in humans. We screened fresh feces from 416 bats (201 Pteropus medius, 165 Rousettus leschenaultii and 50 Taphozous melanopogon) for RVA using rRT-PCR. We detected a prevalence of 7% (95% CI 3.5-10.8) and 2% (95% CI 0.4-5.2) in P. medius and R. leschenaultii, respectively. We did not detect RVA in the insectivorous bat (T. melanopogon). We identified RVA strains similar to the human strains of G1 and G8 based on sequence-based genotyping, which underscores the importance of including wildlife species in surveillance for zoonotic pathogens to understand pathogen transmission and evolution better.

Molecular characterization of rotavirus group A strains circulating prior to vaccine introduction in rural coastal Kenya, 2002-2013

Background: Kenya introduced the monovalent Rotarix® rotavirus group A (RVA) vaccine nationally in mid-2014.  Long-term surveillance data is important prior to wide-scale vaccine use to assess the impact on disease and to investigate the occurrence of heterotypic strains arising through immune selection. This report presents baseline data on RVA genotype circulation patterns and intra-genotype genetic diversity over a 7-year period in the pre-vaccine era in Kilifi, Kenya, from 2002 to 2004 and from 2010 to 2013.

Methods: A total of 745 RVA strains identified in children admitted with acute gastroenteritis to a referral hospital in Coastal Kenya, were sequenced using the di-deoxy sequencing method in the VP4 and VP7 genomic segments (encoding P and G proteins, respectively). Sequencing successfully generated 569 (76%) and 572 (77%) consensus sequences for the VP4 and VP7 genes respectively. G and P genotypes were determined by use of BLAST and the online RotaC v2 RVA classification tool.

Results: The most common GP combination was G1P[8] (51%), similar to the Rotarix® strain, followed by G9P[8] (15%) , G8P[4] (14%) and G2P[4] (5%).  Unusual GP combinations—G1P[4], G2P[8], G3P[4,6], G8P[8,14], and G12P[4,6,8]—were observed at frequencies of <5%. Phylogenetic analysis showed that the infections were caused by both locally persistent strains as evidenced by divergence of local strains occurring over multiple seasons from the global ones, and newly introduced strains, which were closely related to global strains. The circulating RVA diversity showed temporal fluctuations both season by season and over the longer-term. None of the unusual strains increased in frequency over the observation period.  

Conclusions: The circulating RVA diversity showed temporal fluctuations with several unusual strains recorded, which rarely caused major outbreaks.  These data will be useful in interpreting genotype patterns observed in the region during the vaccine era.

Molecular characterization of rotavirus group A strains circulating prior to vaccine introduction in rural coastal Kenya, 2002-2013

Background: Kenya introduced the monovalent Rotarix® rotavirus group A (RVA) vaccine nationally in mid-2014.  Long-term surveillance data is important prior to wide-scale vaccine use to assess the impact on disease and to investigate the occurrence of heterotypic strains arising through immune selection. This report presents baseline data on RVA genotype circulation patterns and intra-genotype genetic diversity over a 7-year period in the pre-vaccine era in Kilifi, Kenya, from 2002 to 2004 and from 2010 to 2013. Methods: A total of 745 RVA strains identified in children admitted with acute gastroenteritis to a referral hospital in Coastal Kenya, were sequenced using the di-deoxy sequencing method in the VP4 and VP7 genomic segments (encoding P and G proteins, respectively). Sequencing successfully generated 569 (76%) and 572 (77%) consensus sequences for the VP4 and VP7 genes respectively. G and P genotypes were determined by use of BLAST and the online RotaC v2 RVA classification tool. Results: The most common GP combination was G1P[8] (51%), similar to the Rotarix® strain, followed by G9P[8] (15%) , G8P[4] (14%) and G2P[4] (5%).  Unusual GP combinations—G1P[4], G2P[8], G3P[4,6], G8P[8,14], and G12P[4,6,8]—were observed at frequencies of <5%. Phylogenetic analysis showed that the infections were caused by both locally persistent strains as evidenced by divergence of local strains occurring over multiple seasons from the global ones, and newly introduced strains, which were closely related to global strains. The circulating RVA diversity showed temporal fluctuations both season by season and over the longer-term. None of the unusual strains increased in frequency over the observation period.   Conclusions: The circulating RVA diversity showed temporal fluctuations with several unusual strains recorded, which rarely caused major outbreaks.  These data will be useful in interpreting genotype patterns observed in the region during the vaccine era.